Characteristics of different glycoside hydrolase family containing enzymes with a demonstrated xylanase activity.
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Barely three months into the new year and we are happy to announce a monumental milestone reached - 150 million downloads.
\n\nThis achievement solidifies IntechOpen’s place as a pioneer in Open Access publishing and the home to some of the most relevant scientific research available through Open Access.
\n\nWe are so proud to have worked with so many bright minds throughout the years who have helped us spread knowledge through the power of Open Access and we look forward to continuing to support some of the greatest thinkers of our day.
\n\nThank you for making IntechOpen your place of learning, sharing, and discovery, and here’s to 150 million more!
\n\n\n\n\n'}],latestNews:[{slug:"webinar-introduction-to-open-science-wednesday-18-may-1-pm-cest-20220518",title:"Webinar: Introduction to Open Science | Wednesday 18 May, 1 PM CEST"},{slug:"step-in-the-right-direction-intechopen-launches-a-portfolio-of-open-science-journals-20220414",title:"Step in the Right Direction: IntechOpen Launches a Portfolio of Open Science Journals"},{slug:"let-s-meet-at-london-book-fair-5-7-april-2022-olympia-london-20220321",title:"Let’s meet at London Book Fair, 5-7 April 2022, Olympia London"},{slug:"50-books-published-as-part-of-intechopen-and-knowledge-unlatched-ku-collaboration-20220316",title:"50 Books published as part of IntechOpen and Knowledge Unlatched (KU) Collaboration"},{slug:"intechopen-joins-the-united-nations-sustainable-development-goals-publishers-compact-20221702",title:"IntechOpen joins the United Nations Sustainable Development Goals Publishers Compact"},{slug:"intechopen-signs-exclusive-representation-agreement-with-lsr-libros-servicios-y-representaciones-s-a-de-c-v-20211123",title:"IntechOpen Signs Exclusive Representation Agreement with LSR Libros Servicios y Representaciones S.A. de C.V"},{slug:"intechopen-expands-partnership-with-research4life-20211110",title:"IntechOpen Expands Partnership with Research4Life"},{slug:"introducing-intechopen-book-series-a-new-publishing-format-for-oa-books-20210915",title:"Introducing IntechOpen Book Series - A New Publishing Format for OA Books"}]},book:{item:{type:"book",id:"4560",leadTitle:null,fullTitle:"Autoimmunity - Pathogenesis, Clinical Aspects and Therapy of Specific Autoimmune Diseases",title:"Autoimmunity",subtitle:"Pathogenesis, Clinical Aspects and Therapy of Specific Autoimmune Diseases",reviewType:"peer-reviewed",abstract:"Autoimmunity is defined as an immune response against a self-antigen. 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The aim of this chapter is to critically reflect on definitions used in different disciplines during the procedure of risk management. Knowledge management is an important part of risk management and can be defined as a collaborative and integrated approach to the creation, capture, organization, access, and use of an intellectual asset [1]. This definition underlines the importance of knowledge management in risk management when different disciplines work together to identify the hazard, assess the risk, and finally predict mitigation mechanism [2]. To facilitate communication between different disciplines, we compared how risk management was approached in different disciplines. We recognized that harmonization of these approaches or definitions would be contraproductive as it would undermine the variety of knowledge and the tasks and perspectives of the different disciplines during the process of risk management. We, therefore, suggest to widen the understanding through appreciation of these differences between disciplines and not to harmonize definitions.
The following disciplines were involved: public health, psychology, environmental health, occupational health, engineering, sociology, and medicine. The selection was made to get a wide variety of disciplines working in different areas but all with a link to risk and risk management. All selected participants have coauthored this chapter. They were recognized experts of risk‐related disciplines. They expressed their opinions and synthetized conclusion in a reiterative process. Each scientist was asked to present his/her own views on the given topics. The following questions were developed to get comparable responses from the participants: What is hazard and risk? How is hazard/risk assessed and which practice of hazard identification and risk assessment is used? and How is risk perception defined? The results were summarized, commented, and discussed by all authors. This method is appropriate as it allows and discusses different opinions. The aim was not to agree on one set of definitions, but critically reflect on the discipline‐related definitions of hazard, risk, and risk perception, and their assessments.
Risk is human being’s attempt to understand and deal with life’s dangers [3]. Thus, the main reason for talking about hazard and risk is to have a sufficiently accurate perception of the situation to make decisions and manage situations in a manner minimizing the probability of adverse effects. In some instances, these decisions are strictly personal and have implications for the individual only, but in other cases, the decision may have implications for larger groups of people, even for the whole population, or for the environment. Disciplines predominantly dealing with numbers and quantifications define risks based on a calculable phenomenon; biological, natural, and technological scientists define risks as objective reality (mostly also in quantitative ways); sociologists view it as a social and cultural construct, whereas psychology looks at it as a cognitive and behavioral phenomenon. Each discipline commonly utilizes their own terms about risks, while keeping different perspectives on what it is [4]. Also, risk communication is hampered by this semantic ambiguity not only in the communication between stakeholders and lay people, but also between different scientific disciplines working together to manage risk [4, 5].
Knowledge management plays an important role in risk issues, for example risk analysis and risk regulations, and knowledge transfer and knowledge sharing are important parts in risk communication. Explicit knowledge is easier to communicate which clarifies the particular problem with newly emerging risks, where explicit or generalized knowledge is unfortunately not available [6].
In the historical perspective, no notion of risk is to be found in traditional cultures: preindustrial hazards or dangers like famines, plagues, or natural disasters were experienced as pregiven. They came from “others”—gods, nature, or demons [7]. However, when carefully reinterpreting the historical perspective, it appears that the notion of risk was already there, albeit implicitly, because one does not have to know the origin of a hazard in order to apply mitigation measures to avoid harm and suffering. One could even argue that sacrificing a virgin to please the god to avoid plagues or nature catastrophes involved an understanding and/or management of a hazard. It may well be that preventive actions taken today will in the future be regarded as similarly useless and surprisingly little evidence‐based as sacrificing virgins to prevent plagues is regarded today.
In the historical perspective, first with the beginning of societal attempts to control risk, and particularly with the idea of steering toward a future of predictable security, the consequences of risk became political issues. Thus, it is a societal intervention—in the form of decision‐making attempts to transform incalculable hazards into calculable risks.
Nowadays, it is necessary to separate the notions of risk and hazard. Knowledge about the hazard should be present before labeling any event as “risky.” Hazard can be defined as an event [8] but it can also be considered as a condition or factor with a potential for causing an event, thus, as a synonym to danger. In this way, hazard is a qualitative term that tells whether exposure to a chemical or drug or certain behavior such as physical inactivity has the potential to cause an undesirable outcome on human health or other things we value, e.g., the environment. The evaluation of an event as a hazard is a mix of objective and subjective data, with the latter depending on individual or at least cultural preferences. The scientific component of the evaluation of the hazard aims to be objective and with a dichotomous (qualitative) outcome, namely being hazardous or not. Scientific uncertainty adds to complexity, if for instance studies on the carcinogenicity of a chemical are controversial, which may add some subjective elements (different researchers interpreting the same studies in different ways) and a categorical scale replacing the dichotomous one to express the level of scientific uncertainty. Nevertheless, researchers then continue to collect further evidence until ultimately the hazard can be established or rejected. Objectively, hazards can be fatal or life‐threatening, leading to disability or only to temporary discomfort; hence, classified according to dimensions of impact on life and of reversibility. The assessment of severity is a quantitative part of hazard evaluation, and the subjective acceptance is the qualitative part. It is subjective because it is the individual’s own judgment reflecting their values and preferences.
On the basis of these facts, a dichotomous hazard will be transformed into a quantitative risk term [9]. In all disciplines, there are two most known concepts of risk definition: the probability of occurrence and severity of the undesirable outcome. Under this approach, risk is the probability function that reflects in quantitative terms the likelihood that a hazard manifests itself while as we have alluded to earlier, the undesirable outcome is the hazard.
Normally, scientific risk assessment should be performed before labeling any event as “risky.” Identification of a hazard is the first step in the risk assessment process. Before identifying the hazard, potential disease or outcome clusters need to be found. For example, before 1989 only one disease outbreak per year was identified in a population of over 60 million people in the Philippines. A surveillance system was set up in 1989 and in 1995 more than 80 disease outbreaks were identified [10]. This means that risks cannot be described as such unless there are procedures to identify or measure outcome clusters or hazards (perceived or real) and our vulnerability to them. Another point worth mentioning is that if you do not know the hazard, you cannot perceive the related risk. The second stage of the risk assessment process entails an estimate of the associated level and extent of potential harm which together with the expected probability of an unwanted event are important, because the evaluation of the acceptability of the options for mitigating the identified risk will usually depend on how much harm the hazard we identify can be estimated to make. For the assessment procedure, two forms of assessment are discussed in detail: the technical procedure and the observational approach.
In the technical procedure like
In the observational approaches of
Risk assessment in
Medical and environmental risk assessments to guide risk management become increasingly challenging, when certain exposures have both risks and benefits, or when the hazard is intended or inherent in a specific scenario. Medical application is a common example of balancing benefit and harm. The use of computed tomography (CT) with its high resolution can clearly lead to better diagnosis and planning of treatment and then becomes lifesaving, but given its exposure to ionizing radiation, a well‐known carcinogen, endorses recommendations that unnecessary examinations need to be avoided and optimal dose adjustment, for example for children, is to be applied [15]. However, there may clearly be a huge risk related to avoiding the hazard of undergoing a CT examination, for instance, due to a delayed detection of cancer. Also, in environmental health not all hazards are entirely avoidable, but risk assessment can guide policy decisions insofar as where to set priorities for an acceptable level of risk and of how much risks can be reduced.
Identifying hazard and severity of a damage has direct consequences for risk perception: “Perception is a process by which individuals select, organize and interpret stimuli to generate a coherent and meaningful picture” [16]. In contrast to risk assessment, which can have a scientific basis with a structure and procedures, risk perception is subjective, involves affects and there are many factors that can influence the way a risk is perceived.
Literally, risk cannot be perceived. Therefore,
From the rational point of view, to evaluate a risk, you need to know something about the hazard, assess probabilities as well as consequences of the negative outcome. In fact, however, intuitive risk judgment has a strong affective component, and it is associated with moral concerns and may neglect any probability consideration in risk appraisal. Doing something about your personal risk depends on how you understand the risk. This is a subjective exercise including the compilation of the more objective information on hazard and risk in combination with individual assessments on severity of risk and potential side effects, and last but not least on personal values and preferences.
From the
All risk concepts of the different disciplines have one element in common; the distinction between reality and uncertainty. Figure 1 illustrates the tasks of the different disciplines in the process of risk management. Engineering and occupational health focuses on hazard and risk identification (explicit knowledge). Sociology looks at the risk on humans and society (social knowledge). Psychology works with risk perception and manages risk on a personal level (individual knowledge). The latter two disciplines rely on the first to identify and describe risk as objective as possible, and the former depend on the psychology and sociology to translate their observations and calculations into something usable for individuals and society. Therefore, it is essential that these disciplines keep their definition and taxonomy of risk knowledge. However, interaction and knowledge sharing is important for the overall risk management process.
Concepts of considered disciplines while defining risk.
The engineer tells the occupational hygienist technical details for the risk assessment; the occupational hygienist communicate risk assessment results to medicine to allow the best treatment for the exposed individual; the doctor needs to explain the information to the patient. Finally, the patient should perceive the risk in that manner to do the right action. Already for a straightforward treatment, a long chain of knowledge transfer needs to work. However, risk assessment and management to reduce the risks is rarely straightforward, especially when scientific uncertainty and, at the same time, competing benefits and risks come into play. A recent example is management of potential risks related to the use of electronic cigarettes [22, 23], for which on the one hand, long‐term adverse health effects are expected, but on the other hand, electronic cigarettes are also expected to be safer than conventional cigarettes to facilitate to quit smoking. Public health researchers mainly request strict regulation to minimize potential future health effects and avoiding electronic cigarettes to become a new socially acceptable way of smoking, especially among youngsters, and thereby torpedoing the efforts for achieving a smoke‐free environment.
Therefore, it is very important to understand underlying terminology from different disciplines. But even more important is to understand their tasks and their views on the topic. For example, the role of sociology “to explain why errors occur but not the truth behind them” clarifies that communication is more important for the sociological perspective than the risk assessment procedure itself, even though both parts are necessary for the overall risk management. If these different views are not taken into account, conflicts and misunderstandings can happen.
In knowledge management, knowledge creation tools were often criticized. One critique is that most tools hide or eliminate important contextual information [24]. Furthermore, it could be shown that individual communication skills have more importance for perceived quality of risk knowledge sharing than the used technical systems [6]. Additionally, lack of time or awareness for the importance of sharing knowledge, missing communication skills, as well as differences in education and culture are seen as the most important barriers for interdisciplinary work [25]. In our opinion, collaborating researchers need to understand their used terms but also have to understand why there are differences. It is very important to know the terminology, tasks, and perspectives from different disciplines. Different terminology can be dealt with in a wiki development, a website that provides collaborative work on terminologies. However, further research is necessary on how to deal with different discipline‐related aims or perspectives in the process of risk management.
Most differences between the disciplines are dealing with risk assessment. All disciplines have the theoretical wish to estimate the real quantitative risk and all disciplines agree that this is difficult to achieve or sometimes not even possible. Disciplines typically using probabilistic approaches, such as engineering or occupational health, define risks mathematically and more objectively. Consequently, these disciplines emphasize the importance of external validity and standardized procedures. Observational research is often connected with a black box phenomenon and is sometimes evaluated as giving less support to evidence than experiments. The presentation of results is more complex and difficult to understand and to trust. Consequently, in these disciplines, problems in objectivity and communication are more obvious. The cognitive approach seen in psychology and social sciences focuses more on the perception of risk. They evaluate the understanding of different risk presentations and look into emotions and cognitive processes while collecting risk assessment information. Due to the fact that risk assessment is seen as less objective, risks are seen as expectations or predictions. However, all disciplines agree that risk assessment should be as objective as possible. To allow for this, evidence‐based information must be used to identify hazards and to assess dose‐response relationships, while exposure assessment should be based on documented, preferably quantitative, measurable, and representative data.
There is a broad common denominator between the disciplines; hazard is a negative event or condition; for most risk definitions, probability and severity of the risks are important; and finally risk perception is seen as subjective and a mental construct. Risk assessment should be evidence‐based, preferably quantitative, measurable, and based on representative data. Assessment of concerns and perceptions is important as well but should be done separately.
Differences can be seen with regard to risk assessment between disciplines with cognitive and probabilistic approaches. However, differences are connected to the interpretation and terminology but not to procedures. Coping with scientific controversies is an important factor in risk management. Different scientific institutions often come to different conclusions and it is easy to select a specific opinion that supports only one view of risk. A transparent risk assessment framework considering different scientific perspectives is important to deal with controversies in risk science.
Knowledge management in risk management needs to account for different use of terminologies by different disciplines. It is important to consider the diversity of tasks and perspectives of various fields when defining terminologies and distributing work. A transparent risk assessment process can only be ensured with an acceptance and appreciation of terminologies and perspectives from different disciplines.
Increasing energy costs and environmental concerns have pushed the global demand for sustainable renewable fuels. The impacts of plant biomass gain particular interest due to their availability as the most abundant raw material worldwide and certainly play an important role because of its significant role as a renewable source of energy [1]. Plant biomass refers to lignocellulosic biomass and its growing demand for the more effective utilization appears to evolve as one of the most important area with great industrial interest. Lignocellulose is composed of the structural polymers of cellulose, hemicellulose, pectin, and lignin. Cellulose is the most abundant polysaccharide in nature followed by hemicelluloses. Xylan is a major structural component of hemicullose and makes up 20–40% of total plant biomass [1].
Various hydrolyzing enzymes are required to degrade lignocellulosic biomass. Carbohydrate-active enzymes, the second largest group of industrial enzymes are sourced from animals, plants, and microorganisms. The hydrolytic enzymes make up nearly 75% of the total extent of industrial enzymes worldwide [2]. Efficient degradation of plant biomass remains a major challenge that requires the availability of enzymes for the hydrolysis of lignocellulosic biomass. Biomass can be efficiently degraded by combining multiple enzymes that hydrolyze complex polysaccharides into fermentable sugars under ideal industrial conditions. These enzymes must be active during a wide range of conditions, such as high temperature and pH [3]. Xylanases are a crucial group of depolymerizing enzymes used for the hydrolysis of the xylan that is a major component of hemicellulose. There is a critical need for thermophilic xylanases operating more efficiently at higher temperatures than current commercially available ones. Xylanase producing thermophilic microorganisms are of prime importance and well-suited for industrial applications. Therefore, there is growing interest in exploring thermophilic microorganisms from extreme environment for biotechnological applications toward biomass degradation. Because of their biotechnological characteristics, xylanases are most often produced from microorganisms for commercial applications. Recently, there has been much industrial interest in xylanases for biofuel production, chemical and pharmaceutical industries, wood pulp bioleaching, papermaking, the manufacture of food and beverages, and animal nutrition. Let us look briefly at the genesis and some promising industrial uses of xylanases.
Lignocellulosic biomass is a potential raw material and its growing demand for the more effective utilization appears to evolve as one of the most important technologies with great industrial interest. Hemicellulose is a complex of polymeric carbohydrates including xylan, xyloglucan (heteropolymer of d-xylose and d-glucose), glucomannan (heteropolymer of d-glucose and d-mannose), galacto-glucomannan (heteropolymer of d-galactose, d-glucose and d-mannose) and arabinogalactan (hetero-polymer of d-galactose and arabinose) [4]. Xylan is a major structural polysaccharide found in the cell walls of plants, in which they may constitute more than 30% of the dry weight [5].
The structure of xylan holds a backbone of β-1,4-linked xylopyranosyl residues with an equatorial configuration and a diversity of substituted groups such as arabinose, acetyl, glucuronic acids, ferulic acid, and p-coumaric acid [6]. However, the structure of xylan is variable, ranging from linear 1,4-β-linked polyxylose sugars other than d-xylose, but the main chain of xylan is analogous to that of cellulose, composed of d-xylose instead of d-glucose. Moreover, xylan interacts with lignin and polysaccharides through covalent and non-covalent linkages, respectively. Different types of covalent linkages are responsible to interconnect xylan and lignin in the secondary cell wall [7]. These covalent interactions include glycosidic linkages between xylopyranosyl and p-coumaric acid and ester linkages between arabinofuranosyl residues and p-coumaric acid or ferulic acid. Feruloyl residues in arabinoxylans are known to be bridging units between xylan and lignin. The distribution pattern of the substituents on xylan affects a series of functional properties, including their solubility, interactions with other polymeric cell wall substances, degradability by enzymes, and solution behavior [8]. In addition, a relationship between the chemical structure of xylan results in a certain degree of complexity of xylan-containing materials, that may have several different xylan polymers of related structures but differ by more or less important features [8].
Xylanases are a crucial group of depolymerizing enzymes used for the hydrolysis of the xylan that is a major component of hemicellulose. Enzymatic depolymerization of hemicellulose to monomer sugars needs the synergistic action of multiple enzymes. These enzymes include endo-xylanase (endo-1,4-β-xylanase), β-xylosidase (xylan-1,4-β-xylosidase), α-glucuronidase (α-glucosiduronase), α-arabinofuranosidase (α-l-arabinofuranosidase) and acetylxylan esterase. Among them endo-xylanases and β-xylosidases are the two key enzymes responsible for the hydrolysis of xylan. Endo-xylanases randomly cleaves the xylan backbone into xylo-oligosaccharides, while β-xylosidases further hydrolyze the xylo-oligosaccharides from non-reducing end into xylose monomers. The removal of side groups is catalyzed by α-d-glucuronidases, α-l-arabinofuranosidases, ferulic acid esterases, acetylxylan esterases and p-coumaric acid esterases [9, 10].
Initially xylanases were classified into two groups, those with low molecular weight (less than 30 kDa) and basic isoelectric points (pI), secondly those with high molecular weight (greater than 30 kDa) and acidic pI. However, this classification system was unable to classify most of the recently discovered xylanases [11]. Afterward, another classification system was introduced that were based on the comparisons of primary structure of the catalytic domains and these enzymes were grouped into families based on related sequences. This classification system now considered the standard means for the classification of enzymes including xylanases. In addition, this classification system gave an extra edge that classifies the glycosidases in general [11]. The most extensive group of enzymes is “Glycoside hydrolases” that refers to catalyze the glycosidic bond cleavage between carbohydrates or between carbohydrate and non-carbohydrate moiety. In glycoside hydrolases (GH) families, some family protein folds are more conserved than their amino acid sequences, and these families are further grouped into clans. Presently, 14 different clans have been proposed (GH-A to GH-N), with most clans encompassing two or more than two families [11].
According to the information provided in the Carbohydrate-Active Enzymes Database (CAZy), xylanases have been classified into 13 families, however only the GH10 (formerly F) and GH11 families (formerly G) with exclusive activities for endo-β-xylanase in them. The difference between these two families based on sequence, different catalytic properties, substrate specificity, three-dimensional structure and mechanism of action [11, 12]. Besides the GH family 10 and 11, xylanases activity are also found in families of GH5, GH7, GH8, GH16, GH26, GH43, GH52 and GH62 [11, 13]. For the reason that some bifunctional enzymes are containing two catalytic domains, for example xylanases having domain of family GH10 or GH11 and it contains a domain of glycosidase as well. Among the other families, GH8 xylanases act solely on xylan whereas GH5, GH7, and GH43 xylanases also show activities as endo-glucanases, licheninases or arabino-furanosidases. Therefore, the enzymes with xylanase activity are solely not only confined to families GH10 and GH11 but also expanded to include other families like GH5, GH7, GH8, GH16, GH43, GH52, GH62 [11].
Xylanases belongs to GH families 10 and 11, which hydrolyze glycosidic bonds by acid base-assisted catalysis through a double displacement mechanism leading to retention of anomeric configuration at the cleavage site [14]. The xylanases from GH family 10 belongs to clan GH-A and the crystal structures display an (α/β)8 barrel fold or “salad bowl” shape with extended loops creating a catalytic cleft that contains at least four to seven xylose-binding subsites [15]. The catalytic site contains two glutamate residues, one acting as a nucleophile and the other as an acid/base catalyst. Catalytic amino acids and enzymatic mechanism are conserved, presenting a domain for catalysis of 250–450 amino acids. From the biochemical point of view, most of them have high molecular weight though there are reports of low molecular weight enzymes [16]. The values of their pI are generally alkaline (8.0–9.5), however, some also have acid values and all of them sustain the same three-dimensional structure. Most of the substrate binding subsites are highly conserved in xylanases, but the affinity differences between these subsites significantly affect their mode of action, as well as substrate and product preferences [17]. As heat stability has great concern in commercial usages of xylanases. For this purpose, a number of studies analyzed the crystal structures of thermostable xylanases. Intra- and intermolecular interactions in structural topography such as disulfide bond and hydrogen bond, compact the overall fold and stabilized N and C terminal end, fusion with CBM (carbohydrate-binding motif) and lower B-factor have been proposed to bestow the enzyme for increased heat stability [18].
The xylanases from the GH11 family belongs to clan GHC. It displays exclusive substrate specificity toward xylose containing substrates and a preference for insoluble polymeric substrates. The structure of GH11 is highly homologous and contains a single major α-helix and two extended pleated β-sheets which form a jelly-roll fold [19]. The structural features include a compact globular structure and a thumb-like structure as an 11-residue long loop that connects β-strands β8 and β7, and a long cleft that spans the entire molecule and contains the active site [20]. The catalytic machinery is composed of two glutamate residues, acting as a nucleophile and an acid/base catalyst, located in the middle of the long cleft [19]. Moreover, catalytic amino acids and enzymatic mechanism of GH11 are conserved and presenting domains for catalysis of 180–200 amino acids that fold into β-sheet conformation curved on itself.
GH 5 is the largest glycoside hydrolase family with varying activities including endo-1,4-β-xylanase. It hydrolyzes the β-1,4 xylan chain at a specific site directed by the position of an α-1,2-linked glucuronate moiety. The structural analysis XynA (of the family 5 xylanase) showed that, the catalytic domain displayed a common (β/α)8 barrel fold [21]; whereas, the β-barrels aligned well with those of another family 5 enzyme. The α-helices and loops were different, showing variances in the positioning, length and orientation. The xylanases belongs to family GH8 are classified in clan CH-M also contains endo-1,4-β-xylanase along with other glycoside hydrolase enzymes. It has also the aptitude to hydrolyze the β-1,4 xylan chain and exhibits the (α/α)6 barrel structure formed by six inner and six outer α helices [22]. Similarly, the GH26 are the member of the clan CH-A and exhibits the (β/α)8 structure. This family contains different glycoside hydrolase enzymes including β-1,3-xylanase, capable of hydrolyzing β-1,3-xylan. Activity, mechanisms and the structure of other member of glycoside hydrolase enzymes are listed in Table 1.
GH family | Fold | Clan | Mechanism | Nucleophile/proton donor | Xylanase Activity | PDB No.* |
---|---|---|---|---|---|---|
GH5 | (β/α)8 | CH-B | Retaining | Glu/Glu | Endo-β-1,4-xylanase (EC 3.2.1.8), Arabinoxylan-specific endo-β-1,4-xylanase (EC 3.2.1.-) | 2Y8K 5G56 4U3A |
GH7 | β-jelly roll | CH-B | Retaining | Glu/Glu | Endo-β-1,4-glucanase (EC 3.2.1.4), Endo-β-1,3–1,4-glucanase (EC 3.2.1.73) | 1EG1 3OVW |
GH8 | (α/α)8 | CH-M | Inverting | Asp/Glu | Endo-1,4-β-xylanase (EC 3.2.1.8) | 1H13 1XW2 |
GH10 | (β/α)8 | CH-A | Retaining | Glu/Glu | Endo-1,4-β-xylanase (EC 3.2.1.8), Endo-1,3-β-xylanase (EC 3.2.1.32) | 4QCE 1NQ6 1 W32 |
GH11 | β-jelly roll | CH-A | Retaining | Glu/Glu | Endo-1,4-β-xylanase (EC 3.2.1.8), Endo-1,3-β-xylanase (EC 3.2.1.32) | 3WP3 1YNA 1XNK |
GH30 | (β /α) 8 | GH-A | Retaining | Glu/Glu | Endo-β-1,4-xylanase (EC 3.2.1.8), Endo-β-1,4-xylanase (EC 3.2.1.136), β-xylosidase (EC 3.2.1.37) | 4FMV 4FMV |
GH43 | 5-fold β-propeller | GH-F | Inverting | Asp/Glu | Xylanase (EC 3.2.1.8), β-xylosidase (EC 3.2.1.37) | 5GLN 2EXJ |
Characteristics of different glycoside hydrolase family containing enzymes with a demonstrated xylanase activity.
PDB, Protein data base number.
Demystifying definitional issue for common understanding, the xylanases are enzymes commonly found in microorganisms, marine algae, protozoans, snails, crustaceans, insects, seeds, plants, and other natural sources [23]. Recently, there has been much industrial interest in xylanases for wood pulp bioleaching, papermaking, the manufacture of food and beverages, animal nutrition, and bioethanol production. Because of their biotechnological characteristics, xylanases are most often produced from microorganisms for commercial applications.
Nature is replete with myriad microorganisms producing enzymatic complexes that degrade cellulose and hemicellulose releasing sugars, used for attainment of products with high economical value [24]. Microbial xylanases are of prime importance in industrial application. Most of commercial enzymes are accrued from mesophilic microorganisms. The thermostable enzymes from thermophilic micro-organisms can better meet the need of high temperatures in the industrial processes for preparing end products. Of course there is a growing interest for multiple studies in exploring the importance of enzymes producing thermophilic microorganisms in relationship with biotechnological application. The microorganisms being extremophilic in nature can survive and thrive in extreme environments on account of which thermo-stability is provided to industrial processes. Biological sources including bacteria, fungi and yeasts have been reported as xylanase producing organisms in a natural process.
Xylanase producing thermophilic bacteria are found in variegated environments and the recent one was isolated in Tunisian hot springs. Various thermophilic
In comparison with the bacteria, the filamentous fungi have been in use as most potent industrial enzyme producers for the last five decades. Filamentous fungi are exuberant producers of xylanolytic enzymes in medium being used for the purpose. The genomes of lignocellulolytic fungi like for example
Other thermophilic fungus like genus
In the field of biotechnology, the thermophilic micro-organisms from archeal domain have been reported/isolated with ability to express enzymes that can tolerate high temperatures (80–115°C), extreme pH, and high salt concentration [38]. These thermophilic enzymes with attribute of hydrolyzing lignocellulosic biomass were characterized, cloned and expressed in various hosts.
Sources | Gene | Substrate | Xylanase activity | References |
---|---|---|---|---|
Xyn11B | Beechwood Xylan | 382.0 U/mg | [36] | |
XynA | Beechwood Xylan | 250.69 U/mg | [41] | |
— | Birchwood Xylan | 5098.28 U/mg | [42] | |
XynA | Beechwood Xylan | 5768 U/mg | [43] | |
XynBS27 | Oat spelt Xylan | 3272.0 U/mg | [44] | |
XAn11 | Birchwood Xylan | 909.4 U/mg | [45] | |
XAn11 | Birchwood Xylan | 415.1 U/mg | [45] | |
XynSL4 | Birchwood Xylan | 244.7 U/mg | [28] | |
Xyn6 | Oat spelt xylan | 172 mg/L | [46] | |
Xyn2 | Birchwood Xylan | 1600 U/mg | [47] | |
MYCTH_56237 | RBB-Xylan* | 1533.7 U/mg | [48] | |
MYCTH_49824 | RBB-Xylan* | 1412.5 U/mg | [48] | |
MYCTH_39555 | Birchwood Xylan | 105.42 U/mg | [49] |
Sources of microbial xylanases with demonstrated activity.
RBB-Xylan, Remazol brilliant blue-Xylan.
To acquire a pure form of a particular enzyme from a given source is challenging. Also it is inconvenient to have cultivation of bacteria or fungi for large scale protein production that often leads to many interfering enzymes. It might need multiple purification steps to get the intended enzymes purified from a pool of proteins which in turn will increase the cost. Therefore, recombinant DNA technology is recommendable for application with success prospects for desired object [50]. Recombinant DNA technology allows large scale expression of enzymes in both homologous and heterologous protein expression. The genes of enzymes with industrial importance were reportedly cloned and expressed in expression hosts in order to enhance specific enzymes production plus improvement in substrate utilization, and other commercially useful properties. Likewise, genes encoding thermophilic xylanases from different sources have been cloned with the objectives of overproduction of the xylanases and changing its properties to suit commercial applications [9].
Although previously it has been reported that the expression of the xylanase genes usually cannot be functionally expressed in
Filamentous fungus is the promising organism for protein expression and its production by fermentation has a long history in industrial area. Even developed other expression systems for recombinant protein expression, fungal expression system also considered an appropriate candidate for the expression [9]. Natural capability of fungal expression system to secrete large amounts of proteins into the medium gave an advantage to this expression system. Furthermore, it has feasibility for functional expression of other xylanases from remote sources by using of native xylanase expressing machinery [7, 9]. Most of the xylanase genes have been expressed in fungi under homologous expression system and frequently used fungus as expression hosts are
Yeasts considered as excellent and attractive host for the expression of heterologous proteins and offer many advantages over the other established expression systems especially in protein maturation [59]. The methylotrophic yeast
In most of the cases xylanases need to undergo some genetic modifications in order to enhance expression level, enzymes activity and that might have some influence on substrate specificity and stability to high temperature and pH. The gene encoding cellulolytic and xylanolytic enzymes are usually regulated by a repressor/inducer system in fungi. Xylanolytic transcriptional regulators have been reported in thermophilic fungi. The strong promoter MtPpdc (pyruvate decarboxylase) recently used for the overexpression of xylanases from
In order to fulfill the demands of industrial requirements, gene mining and protein engineering are applied to develop thermostable xylanases. Although some of thermophilic xylanases were produced from thermophiles but their lower expression levels and specific activities making them unable to be applied efficiently. The higher specific activity with enhanced thermostability of xylanases is therefore needed through genetic engineering. Recently the thermostability of mesophilic xylanase (AuXyn10A from
The enzymatic degradation reaction of insoluble polysaccharides had great importance. However, glycoside hydrolase enzymes often inaccessible to the active site of the appropriate enzymes, such polysaccharides relatively inefficiently. In order to overcome these problems, many of the glycoside hydrolases that utilize insoluble substrates are modular, comprising catalytic modules appended to one or more non-catalytic carbohydrate-binding modules (CBMs) [72]. Two xylanase genes belongs to family GH11 (xynC81 and xynC83) from a thermophilic strain
Moreover, some xylanases bears CBMs specific for cellulose, which probably assist indirectly localization of xylanase to the xylan substrate, since it is in close association with cellulose. The number of characterized fungal xylanases harboring CBM1 module is relatively reduced. It includes xylanases from
The metal ion and chemical reagents had been proved to be one of the critical factors which affected the enzyme activity of xylanases. The effect of metal ions and chemical reagents on the xylanase activities has been determined on various metal ions (Na+, K+, Ca2+, Li+, Co2+, Cr3+, Ni2+, Cu2+, Mg2+, Fe3+, Zn2+, Pb2+, and Ag+) and chemical reagents (SDS, β-mercaptoethanol, ethanol, Triton X-100, and EDTA) at the standard condition. Ca2+, Pb2+, K+, Mn2+, EDTA, β-ME, Cu2+ and Triton X-100 were reported to enhance enzyme activity by 6.4–29.9% [81], while Fe3+, Cd2+, Hg2+, and Ba2+ completely suppressed the xylanase activity. Besides this, the enzyme had certain ability to resist the Fe2+, Mg2+, Ag2+, SDS, ethanol and SDS. Xylanase activity was not inhibited by chelating reagents such as EDTA and EGTA. Moreover, it is predicted that Ca2+ and Mg2+ ions enhance the enzyme activity by stabilizing the enzyme–substrate complex. In contrast, EDTA is a chelating agent and it removes ions from the enzymes, thus inhibits the enzyme activity [7]. More detailed studies are needed in order to understand the mechanistic effect of metal ions on enzyme activity. Similarly, a xylanase activity isolated from
As thermophilic enzymes are preferred over the mesophilic enzymes complements because of high temperatures, which had a great influence on many factors such as decreases contamination risk and viscosity of substrate [82]. In a study carried out with the effect of xylanase activity from
Evaluation of the pH stability is a vital part of any enzyme characterization before it can be exploited commercially. Similarly effect of pH had great influence on the xylanase activity. The effect of pH on extracellular xylanase from
Species | Strain | pH | Temperature | References |
---|---|---|---|---|
TH7C1(T) | 11.0 | 70°C | [26] | |
JAM-AC0309 | 8.0 | 65°C | [86] | |
SL4 | 7.0 | 70°C | [28] | |
WBI | 7.0 | 65°C | [87] | |
F32 | 6.6 | 75°C | [88] | |
Cpt20 | 10.0 | 80 °C | [89] | |
Tpbgl | 3.5 | 95°C | [90] | |
MT4 | 7.0 | 90°C | [91] | |
AN1 | 6.0 | 75°C | [92] | |
Pol6 | 3.0 | 65°C | [93] | |
S582 | 6.5 | 70°C | [94] | |
J18 | 7.0 | 75°C | [95] | |
MEY-1 | 4.5 | 85°C | [96] | |
S168 | 6.5 | 80 °C | [97] | |
B3–11(2) | 5.0 | 50 °C | [98] |
List of xylanase producing microbial species/strains with demonstrated pH and temperature.
Because of their biotechnological characteristics, xylanases are most often produced from microorganisms for commercial applications. The environmental hostility and lethality to most of living organisms due to extreme hot environments is obvious but such factors are counter-productive in the presence of specialized microorganisms. These microorganisms from harsh environments can tolerate high or low temperatures, extremes pH and high concentrations of salts. Based on the unique stability of their enzymes at high temperature, extremes of pH they are expected to be a powerful tool in industrial biotransformation processes that run at harsh conditions. Enzymes derived from extremophiles have great importance to the local enzymes because they can perform industrial processes even under harsh conditions, under which conventional proteins are completely denatured. The extremophile research, the high demands of the biotech industries for tailor-made novel biocatalysts, and the rapid development of new techniques such as genomics, proteomics, metabolomics, directed evolution and gene shuffling will stimulate the development of new industrial processes on the basis of biocatalysts from extremophiles.
Enzymatic hydrolysis of xylan has become attractive due to its biotechnological applications in the food, animal feed, waste treatment, ethanol production, textile, and pulp and paper industries [11]. Xylanases gained its importance for the saccharification process in degradation of lignocellulosic biomass, because xylanases assist the hydrolysis of xylan and ultimately leads to the hydrolysis of hemicellulose and cellulose, to obtain industrially important products [99]. In addition, biofuel production from lignocellulosic biomass has great concern in industrial sectors worldwide. However, biofuel production is still a bottleneck, because the initial conversion of biomass into sugars requires multiple enzymes (including xylanases) with high activity and excellent enzyme properties. Therefore, recent development in biotechnological applications xylanases toward the biomass conversion is on way [100]. Moreover, highly stable enzymes, active under high temperature and wide range of pH, displayed several advantages over the enzymes from mesophilic or neutrophilic origin. For example, highly active xylanases under extreme conditions reduce the contamination risk due to fast reaction rate. In second generation ethanol industries, mild pretreatment of biomass requires to reduce the total costs and sustain the high contents of hemicellulose. However, high dosage of other enzymes is still needed for the complete conversion of hemicellulose. Therefore, the biotechnological application of xylanases especially thermophilic xylanases and its interaction with other enzymes such as cellulases, xylosidases, arabinofuranosidase seems to be an effective in saccharification process.
The use of xylanases, as accessory enzymes, has shown to improve the hydrolysis of xylan and cellulose, and it has contributed to the reduction of enzyme dosage, but it seems to be a substrate dependent reaction [101]. Recently, less severe pretreatments of lignocellulosic biomass are gaining popularity, thus, hemicellulase characterization and studies regarding synergism of cellulases and xylanases, can contribute to reducing pretreatment severities and enhancing glucose and xylose release [102]. Xylanases are very important in bioconversion of xylan into value added products, such as xylitol. Xylitol is used in soft drinks, candies, ice cream, chewing gum and various pharmaceutical products. Xylitol have key role in sweeten food products and used as a natural sweetener in toothpaste. Xylanases have great importance in the bio-bleaching of wood pulp and in the bioprocessing of textiles.
Xylanases are very useful in manufacturing of animal feed. Xylanases reduce the viscosity and enhance the absorption rate by degrading the starch polysaccharides in rich fiber and barley based feeds. Pre-treatment of agricultural silage and grain feed employed with xylanases increases the nutritional value and improves the feed digestion in ruminants. Similarly, feed supplementation combined with xylanases for broiler diets, not only increases growth performance like weight gain but also helpful in the yield production of poultry products.
Conclusively, the xylanases have potential applications in a wide range of industrial processes, covering all sectors of industrial enzymes markets. Arguably, these are attractive for research studies and deeper investigation with aims to explore dividends and utility of these useful products in industrial context in relation to industrial enzymes producing organisms.
Microbial xylanases are gaining importance in industrial applications. The thermophilic microorganisms are of interest in the field of biotechnology because of their ability to express enzymes that tolerate high temperature and pH. The thermophilic bacteria, and an archaeal species, there are also filamentous fungi that grow in diverse environments and produce xylanase. New recombinant DNA technology can be used to express xylanases in both homologous and heterologous host organisms. Compared to
This study was supported by National Natural Science Foundation of China (31570067).
The authors declare no conflict of interest.
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In this context and based on the approaches of the Theory of Entrepreneurship, it discusses what is meant by social entrepreneurship and the impact of social capital in the creation of such enterprises.",book:{id:"5145",slug:"social-enterprise-context-dependent-dynamics-in-a-global-perspective",title:"Social Enterprise",fullTitle:"Social Enterprise - Context-Dependent Dynamics In A Global Perspective"},signatures:"Virginia Barba-Sánchez and Ericka Molina-Ramirez",authors:[{id:"179639",title:"Prof.",name:"Virginia",middleName:null,surname:"Barba-Sánchez",slug:"virginia-barba-sanchez",fullName:"Virginia Barba-Sánchez"},{id:"180720",title:"MSc.",name:"Ericka",middleName:null,surname:"Molina-Ramírez",slug:"ericka-molina-ramirez",fullName:"Ericka Molina-Ramírez"}]},{id:"50229",doi:"10.5772/62469",title:"Social Entrepreneurship by Community-Based Organizations: Innovations and Learning through Partnerships",slug:"social-entrepreneurship-by-community-based-organizations-innovations-and-learning-through-partnershi",totalDownloads:1878,totalCrossrefCites:0,totalDimensionsCites:1,abstract:"This chapter examines the social entrepreneurship potentials of community-based organizations (CBOs) linked to nongovernmental organizations (NGOs) in the implementation of development programs. 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This approach highlights such side effects as unaddressed (suppressed) discriminatory attitude towards employees with disabilities in enterprises, organisational weakness in dealing with interpersonal conflicts, the lack of competence of the managerial staff and the lack of systematic knowledge on work with personnel. In this case, there is a debatable question of whether the efforts of the state will reach the desired goal, i.e. the fully-fledged work and social integration of the people who the investments are intended for, or continue the traditions of silent social segregation? This study shows that it is necessary to critically evaluate the selected model for fostering businesses to integrate into the labour market, in which the issues of psycho-social welfare and social initiative of enterprises are underestimated.",book:{id:"5145",slug:"social-enterprise-context-dependent-dynamics-in-a-global-perspective",title:"Social Enterprise",fullTitle:"Social Enterprise - Context-Dependent Dynamics In A Global Perspective"},signatures:"Jolita Vveinhardt",authors:[{id:"179629",title:"Prof.",name:"Jolita",middleName:null,surname:"Vveinhardt",slug:"jolita-vveinhardt",fullName:"Jolita Vveinhardt"}]},{id:"50229",title:"Social Entrepreneurship by Community-Based Organizations: Innovations and Learning through Partnerships",slug:"social-entrepreneurship-by-community-based-organizations-innovations-and-learning-through-partnershi",totalDownloads:1878,totalCrossrefCites:0,totalDimensionsCites:1,abstract:"This chapter examines the social entrepreneurship potentials of community-based organizations (CBOs) linked to nongovernmental organizations (NGOs) in the implementation of development programs. 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Although marketing communication studies have long established the effects of corporate credibility on consumer attitudes and behaviors, it is worth noting that corporate credibility comprises three distinct dimensions, namely trustworthiness, expertise and dynamism, which do not necessarily have equal levels of influence on the endogenous variables. Additionally, from a social entrepreneurship perspective, the relationship between corporate credibility and consumer psychology requires a deeper inspection because of the role of religion in charitable and care-giving activities. Most religions stress the importance of spirituality, which may override their concern with the business aspects of the SE. In other words, for religious customers, it is likely that trustworthiness has a higher influence on their attitudes and support intention than expertise and dynamism. These conceptual relationships among corporate credibility, religion and consumer psychology in social entrepreneurship are elaborated in this article through a literature review, followed by the development of a theoretical framework and its associated propositions. 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